[R] ggplot2 reorder factors for faceting

Iain Gallagher iaingallagher at btopenworld.com
Tue Nov 8 12:51:17 CET 2011

Dear List

I am trying to draw a heatmap using ggplot2. In this heatmap I have faceted my data by 'infection' of which I have four. These four infections break down into two types and I would like to reorder the 'infection' column of my data to reflect this. 

Toy example below:


# test data for ggplot reordering
genes <- (rep (c(rep('a',4), rep('b',4), rep('c',4), rep('d',4), rep('e',4), rep('f',4)) ,4))
fcData <- rnorm(96)
times <- rep(rep(c(2,6,24,48),6),4)
infection <- c(rep('InfA', 24), rep('InfB', 24), rep('InfC', 24), rep('InfD', 24))
infType <- c(rep('M', 24), rep('D',24), rep('M', 24), rep('D', 24))

# data is long format for ggplot2
plotData <- as.data.frame(cbind(genes, as.numeric(fcData), as.numeric(times), infection, infType))

hp2 <- ggplot(plotData, aes(factor(times), genes)) + geom_tile(aes(fill = scale(as.numeric(fcData)))) + facet_wrap(~infection, ncol=4)

# set scale
hp2 <- hp2 + scale_fill_gradient2(name=NULL, low="#0571B0", mid="#F7F7F7", high="#CA0020", midpoint=0, breaks=NULL, labels=NULL, limits=NULL, trans="identity") 

# set up text (size, colour etc etc)
hp2 <- hp2 + labs(x = "Time", y = "") + scale_y_discrete(expand = c(0, 0)) + opts(axis.ticks = theme_blank(), axis.text.x = theme_text(size = 10, angle = 360, hjust = 0, colour = "grey25"), axis.text.y = theme_text(size=10, colour = 'gray25'))

hp2 <- hp2 + theme_bw()

In the resulting plot I would like infections infA and infC plotted next to each other and likewise for infB and infD. I have a column in the data - infType - which I could use to reorder the infection column but so far I have no luck getting this to work.

Could someone give me a pointer to the best way to reorder the infection factor and accompanying data into the order I would like?



> sessionInfo()
R version 2.13.2 (2011-09-30)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_GB.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_GB.utf8        LC_COLLATE=en_GB.utf8    
 [5] LC_MONETARY=C             LC_MESSAGES=en_GB.utf8   
 [7] LC_PAPER=en_GB.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.6     

loaded via a namespace (and not attached):
[1] digest_0.5.0 tools_2.13.2

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